Chromosome‐level assembly of the <i>Neolamarckia cadamba</i> genome provides insights into the evolution of cadambine biosynthesis

Zhao, Xiaolan; Hu, Xiaodi; Ouyang, Kang; Yang, Jing; Que, Qingmin; Jiang, Long; Zhang, Jianxia; Zhang, Tong; Wang, Xue; Gao, Jiayu; Hu, Xinquan; Yang, Shenghai; Zhang, Lisu; Li, Shufen; Gao, Wu‐Jun; Li, Benping; Jiang, Wenkai; Nielsen, Erik; Chen, Xiaoyang; Peng, Chang-Cao

doi:10.1111/tpj.15600

Cited by 23 publications

(12 citation statements)

References 98 publications

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“…A genome‐wide analysis of selective sweeps in cultivated Asian lotus was implemented according to previous studies (Li et al., 2013; Zhao et al., 2021). Here, we calculated the genome‐wide distribution of the F ST values and p i ratios for the defined group pairs (WL–SL and WL–RL).…”

Section: Methodsmentioning

confidence: 99%

Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication

et al. 2022

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SUMMARY Nelumbo lutea (American lotus), which differs from Nelumbo nucifera (Asian lotus) morphologically, is one of the two remaining species in the basal eudicot family Nelumbonaceae. Here, we assembled the 843‐Mb genome of American lotus into eight pseudochromosomes containing 31 382 protein‐coding genes. Comparative analyses revealed conserved synteny without large chromosomal rearrangements between the genomes of American and Asian lotus and identified 29 533 structural variants (SVs). Carotenoid and anthocyanin pigments determine the yellow and red petal colors of American and Asian lotus, respectively. The structural genes encoding enzymes of the carotenoid and anthocyanin biosynthesis pathways were conserved between two species but differed in expression. We detected SVs caused by repetitive sequence expansion or contraction among the anthocyanin biosynthesis regulatory MYB genes. Further transient overexpression of candidate NnMYB5 induced anthocyanin accumulation in lotus petals. Alternative oxidase (AOX), uncoupling proteins (UCPs), and sugar metabolism and transportation contributed to carpel thermogenesis. Carpels produce heat with sugars transported from leaves as the main substrates, because there was weak tonoplast sugar transporter (TST) activity, and with SWEETs were highly expressed during thermogenesis. Cell proliferation‐related activities were particularly enhanced in the warmer carpels compared with stamens during the cold night before blooming, which suggested that thermogenesis plays an important role in flower protogyny. Population genomic analyses revealed deep divergence between American and Asian lotus, and independent domestication affecting seed, rhizome, and flower traits. Our findings provide a high‐quality reference genome of American lotus for exploring the genetic divergence and variation between two species and revealed possible genomic bases for petal color, carpel thermogenesis and domestication in lotus.

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Section: Methodsmentioning

confidence: 99%

Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication

et al. 2022

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“…The predicted NcFBP genes were identified as follows: first, the N. cadamba genomic sequences were downloaded from the National Center for Biotechnology Information (NCBI) BioProject database [ 19 ] and BioEdit biological sequence alignment editor software was used to create a local database file. Next, a hidden Markov model (HMM) program was used for gene prediction against the local database through the BlastP method (E value < 10 −10 ).…”

Section: Methodsmentioning

confidence: 99%

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

Que

Liang

Song

et al. 2022

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Neolamarckia cadamba (N. cadamba) is a fast-growing tree species with tremendous economic and ecological value; the study of the key genes regulating photosynthesis and sugar accumulation is very important for the breeding of N. cadamba. Fructose 1,6-bisphosptase (FBP) gene has been found to play a key role in plant photosynthesis, sugar accumulation and other growth processes. However, no systemic analysis of FBPs has been reported in N. cadamba. A total of six FBP genes were identifed and cloned based on the N. cadamba genome, and these FBP genes were sorted into four groups. The characteristics of the NcFBP gene family were analyzed such as phylogenetic relationships, gene structures, conserved motifs, and expression patterns. A cis-acting element related to circadian control was first found in the promoter region of FBP gene. Phylogenetic and quantitative real-time PCR analyses showed that NcFBP5 and NcFBP6 may be chloroplast type 1 FBP and cytoplasmic FBP, respectively. FBP proteins from N. cadamba and 22 other plant species were used for phylogenetic analyses, indicating that FBP family may have expanded during the evolution of algae to mosses and differentiated cpFBPase1 proteins in mosses. This work analyzes the internal relationship between the evolution and expression of the six NcFBPs, providing a scientific basis for the evolutionary pattern of plant FBPs, and promoting the functional studies of FBP genes.

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“… [ 28 ] and Neolamarckia cadamba (Roxb.) Bosser [ 29 ] . The plastid genome from short-reads of C. pubescens had a length of 156,985 base pairs (bp) and a GC content of 37.74%, very similar to other Rubiaceae plastid genomes [ 25 , 30 ] .…”

Section: Contextmentioning

confidence: 99%

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

et al. 2022

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The Andean fever tree (Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82% of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.

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Chromosome‐level assembly of the Neolamarckia cadamba genome provides insights into the evolution of cadambine biosynthesis

Cited by 23 publications

References 98 publications

Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication

Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication

Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba)

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

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